Maximum Parsimony Method for Phylogenetic Prediction
Adapted from “Phylogenetic Prediction,” Chapter 7, in Bioinformatics: Sequence and Genome Analysis, 2nd edition, by David W. Mount. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2004.INTRODUCTION
Maximum parsimony predicts the evolutionary tree or trees that minimize the number of steps required to generate the observed variation in the sequences from common ancestral sequences. For this reason, the method is also sometimes referred to as the minimum evolution method. A multiple sequence alignment (msa) is required to predict which sequence positions are likely to correspond. These positions will appear in vertical columns in the msa. For each aligned position, phylogenetic trees that require the smallest number of evolutionary changes to produce the observed sequence changes from ancestral sequences are identified. This analysis is continued for every position in the sequence alignment. Finally, those trees that produce the smallest number of changes overall for all sequence positions are identified. This method is best suited for sequences that are quite similar and is limited to small numbers of sequences.
